Secondary and Tertiary Structure in Proteins Flashcards
Genetic Code
How the sequence of DNA dictates the sequence of proteins - triplet code
quaternary structure
- interactions between subunits
all folding orders dictated by
primary sequence of the protein
the major secondary structures in proteins
- alpha-helix
- beta-sheet
- beta-turn
- random coils
structure and function
closely tied to one another
determine the structure of proteins
- use X-ray crystalography
X-ray crystallography
- proteins must be collected at high concentrations and crystallized
- crystals exposed to X-rays and diffracted by protein in a way determined by position of chemical bonds within the protein
- diffraction pattern produces 3D image of density of electrons within crystal to determine protein structure. q
Linus Pauling’s solution of the alpha-helix
- contributed to structure of DNA - the way H bonds stabilize alpha-helices in proteins
- The Nature of the Chemical Bond
- proposed alpha-helix and beta-sheet
- establishes hydrophobic face that will interact with other proteins to form a leucine dimer
- proposed triple helix -wrong!
alpha-helix
- hydrogen bonds between C=O and NH stabilize the helix
- one helical turn ~ 3.5 amino acids
- two turns = 7 amino acids
- every 7th amino acid will have R-groups on the same face of the helix - important for protein interaction
Beta-sheet
- hydrogen bonds between C=O and NH stabilize the B-sheet
- remaining C=O and NH can hydrogen bond with another B-sheeet creating B-pleated structures
- flattened sheet instead of helical structure
anti-parallel
- amino group adjacent to carboxy group of next
- more stable and found more commonly
parallel
- all amino termini in same direction
ribbon structure
- idealized drawings of the tertiary structures of several globular proteins (secondary structures)
- coiled regions represent alpha helix and flat arrows indicate beta-structure
Barrel structure
- another way of drawing alpha-helices
- alpha-helix between two beta-sheets
Chou-Gasman table
- propensity of amino acids to form alpha-helix or beta-sheet based on proteins of known sequence and known secondary structure from x-ray crystallography
most likely to be found in alpha-helix
- Glu
- Ala
- Leu
least likely to be found in alpha-helix
- Pro
- Gly
most likely to be found in beta-sheet
- Met
- Val
- Ile
least likely to be found in beta-sheet
- Pro
- Glu
Absolute helix breakers
- proline and glycine
proline
- not in alpha-helix due to its structure
- no H bond because tied up in ring structure.
Chou-Fasman Rules
- are used to PREDICT (not Determine) secondary structure in proteins.
hydrophobic interactions and tertiary structure
- hydrophilic outside to interact with H2O
- hydrophobic inside to not react with H2O
Hydropathy index
- help predict tertiary structure of protein also using sliding window approach
Sliding window
- Consider 5 AA next to each other
- average hydropathy index
- plot
- slide down one AA
Hydropathy plots
- done for whole length of protein
- help determine which regions are hydrophobic or hydrophilic in a given protein
- good sliding window of 9
bars above 0
interior regions of the protein as determined by crystallography
bars below 0
exterior region of the protein as determined by crystallography
A reason why you might expect a hydrophobic portion of a protein to be on the outside of a protein rather than on the inside
- if a protein spans a membrane
- if a portion of the protein is involved in an INTERACTION with another macromolecule through hydrophobic interactions
Homology modeling
- constructing a model of a protein based off known AA seq and known 3D seq of related protein with similar function
- identification of insect olfactory receptors after mammalian receptors identified
hydropathy plots for evolutionary comparisons
- to identify functional homologues
